He's the Doctor
by AgentMaryMargaretSkitz
Summary: What if Leo Fitz isn't the man he thinks he is? What if he isn't even human? What if he's really a time-traveling, two-hearted alien who's lost his memories? (Basically, Fitz is the Doctor)
1. Chapter 1

**So maybe a couple months ago, I sort of came up with this really weird theory that Fitz was, erm, the Doctor. A future incarnation, probably 13th, of the Doctor. I'm not gonna argue about the 12 to 13 regenration, but I'm considering writing it out later. Hopefully you all enjoy it.**

 **I'm setting this during the happier times of SHIELD, except there's probably not Hydra lurking about. So yay!**

 **Also, this is a birthday gift to the person who helped inspire this, fezwearingjellybananas, the Great Crossover Genius. Happy birthday!**

* * *

 _Hyperia Galaxy_

" _Shut the door, shut the door!" The Doctor shrieked franticly as they ran inside the TARDIS._

 _Jemma stopped and grabbed the side of the door. She hesitated, peering out one last time at the beautiful grassy meadow the TARDIS had landed in. It could have been on Earth, had the grass not been a silver color or the horizon a shade of violet. Also, there was the little issue of the bounty hunters shooting at them. That last realization that reminded her of the pressing danger that was coming at them. She slammed the TARDIS door shut and slumped down against them with a huff of exhaustion._

" _What about the girl?" she said, climbing back up to her feet as she remembered how they'd gotten out of the fortress they'd gotten trapped in. "Ellie Oswin, we have to get her back!"_

 _Down at the TARDIS console, the Doctor looked up at her, his eyes full of sadness. Jemma stood at the top of the small staircase that led down to the console. "Doctor, what is it? What happened?"_

" _After they took you out of the cell to interrogate you about me, Ellie and I picked the lock and got out," The Doctor explained sadly. Jemma felt the TARDID begin to take off as he opened a hatch on the floor and started to dig through it. "We ran into some of Sarnim's hunters, and oh we ran. But once we reached the doors to the room you were held in, they were locked. Ellie went back to the control room to unlock them for me. She got them open, but the hunters got to her before she could come back. They killed her, Jemma."_

 _Jemma gasped. When the Doctor had gotten her out of the interrogation room, she'd barely been conscious and he'd needed to carry her. They'd given her some sort of truth drug that made her tell them the answers to every question they asked her. Once it had run its course through her system, it was as though she had run a marathon. She'd only been able to stand and run just a few minutes ago, when they had gotten out of Sarnim's fortress. "Doctor, I'm sorry."_

" _I knew she was going to die, and she was going to do it saving my life. That's how it's always been with my impossible girl," the Doctor muttered wistfully as he emerged from the hatch holding an odd helmet. "Jemma, come down here if you will."_

 _She clamored down the steps and stopping beside the Doctor. He was attaching the strange helmet device to the TARDIS console. Frowning at the thick layer of dust on it, he inhaled and blew at it. A cloud of dust assaulted Jemma's face, making her scrunch up her nose._

" _Sorry, haven't pulled this thing out in a while," the Doctor apologized, rubbing the sleeve of his cardigan against it to remove the dust. "Never thought I'd need to pull it out again though."_

 _Jemma nodded as he continued to fiddle around with the helmet. As he was doing so, the Doctor turned to face her._

" _Jemma," he said, his face stern and serious. "Do you trust me?"_

" _What?"_

" _Do you trust me?" The Doctor repeated as he took her by the shoulders, looking her dead in the eye. "I need to know this, Jemma. I need an answer."_

" _Yes, yes, I do!" Jemma shouted. "Of course I trust you!"_

" _Can I trust you?"_

 _She nodded. "You can. Doctor, what's going on?"_

" _Sarnim is a very, very nasty fellow. I didn't remember who he was until his hunters kidnapped us and brought us to his fortress. He's a very dangerous dealer in the inter-galactic black market. They call him the Harvester."_

" _Why is that?" Jemma questioned as the Doctor pulled out a pocket watch from the hatch in the floor._

" _He likes to take organs of certain, rare species and sell them on the black market," the Doctor explained as Jemma looked at her in horror. "Sarnim wouldn't bother with you. Humans are beneath him, in his opinion. A body of a Time-Lord, on the other hand, is incredibly coveted. If he gets me, then he'll take my organs, my blood, my body. Time-Lords are so few, and even the bodies of dead ones have value."_

 _Jemma looked over at him. "So what can we do to stop him?"_

 _The Doctor looked forlorn. "He won't give up until he dies. Ought to call him Sarnim the One Who Never Gives Up- no, never mind. Too long, too complicated. However, his species don't have particularly long lifespans, so we need to hide out. Unfortunately, he's got some genetic material- my spit, long story, involves me spitting on his face. But he can use this to track me. So we're going to go back to Earth, and I'm going to become human."_

" _How? How can you become human?"_

" _Using this," The Doctor said, slapping the helmet he had brought out. "Put it one, stick this watch in one side- it'll be holding onto my memories for me- and it'll rewrite all my cells, change them from Gallifreyian into good old human ones."_

" _Is it going to hurt?"_

" _You bet," The Doctor replied, nodding. "I've done it before though, so maybe it won't hurt as bad. But Jemma, I need you to watch out for me. I'm not going to know who I am. I won't remember who I am. John Smith isn't a Time-Lord, so he won't have Time-Lord memories. If you can help me get back on my feet once I'm human, help watch out for me, that would be brilliant. Just keep an eye on me, and never lose this," he held up the watch. "It's going to hold my memories. If I open it after I become human, then they come back and I become Time-Lord again. That'll lead Sarnim right to me if he's still alive. But if we wait a year on earth, he'll be dead by then, and you can give me back the memories. Can you do this for me?"_

 _Jemma nodded as he placed the pocket watch in the side of the helmet. She was scared, but she could do this. The Doctor had saved her at the Academy and took her to see the most incredible things. This was the least she could do to pay him back._

" _One thing though," she said, drawing the Doctor's attention over to her. "You can't call yourself John Smith."_

" _Why not, it's always what I call myself!"_

" _You use it so often and it's so common," Jemma frowned. "Wait, have you used it so much that you made it common?"_

" _Perhaps, I don't know."_

 _Jemma sighed. "Anyway, people will know it's fake."_

" _Well, if you don't like it, then how about you pick out a name for me this time," the Doctor argued, taking off his coat and throwing it over the railing._

 _Jemma squeezed her eyes shut, thinking to all the places they'd been together. One of the last places before Sarnim was the future Earth, where they'd met…Leopold XVI of the Silurians. He'd been a good friend to them, as well as a gracious host to them. "Leopold…"_

" _Ooo good, I like it! Very good. For the Silurian leader, right?" The Doctor grinned as Jemma murmured in agreement. "Brilliant, now I just need a last name."_

" _Okay, okay," Jemma kept thinking. "Before that were the Daleks-"_

" _Don't be taking any names from that adventure!"_

" _Wasn't planning on it," she mumbled, shuddering at the memory. "And before that, you took me to the twenties, and we stopped a Zygon attack with F. Scott Fitzgerald."_

 _An idea hit her, and Jemma snapped her fingers. "Leopold Fitzgerald! No, wait, Leopold Fitz! That sounds better."_

" _Leopold Fitz," The Doctor mused, grinning. "I think I like that."_

" _Me too."_

 _The Doctor gave her a sad smile. "We'll be landing in Anne Weaver's office soon. When we do, get out and tell her everything. I won't be the Doctor, I'll be Leopold Fitz then, and I won't know her. Get her to help you with me, okay?"_

" _Okay," agreed Jemma._

 _She stepped forward and hugged him. "Good-bye, Doctor."_

" _It's not good-bye," he reassured her. "I'll be back, Jemma. Good luck."_

 _With that, he put on the helmet and flicked a switch. For a moment, there was nothing, and then he collapsed to his knees, screaming and shouting._

* * *

 _2012, SHIELD Base, New York_

" _Everybody evacuate now!" The intercoms screamed as scientists began to hurry toward the staircases and elevators leading to the underground bunkers._

" _C'mom, Simmons, let's go!" The Doctor- no, Fitz- was dragging her along toward the passage. It had been a year since they'd come back to Earth, and she still found it hard to see him as Fitz, and not the Doctor. He adjusted to life well on Earth, blissfully ignorant of who he really was._

 _Suddenly, something hit the building and shook it hard. Jemma felt herself tumble forward. As she hit the floor, Jemma caught sight of the pocket watch with the Doctor's memories skidding across the floor. She'd put it on a chain to hang around her neck, but had taken it off today while they were conducting an experiment. Pushing herself up, she started to crawl over to it, but Fitz held her back._

" _It's not worth it, we have to run!" he told her, dragging her toward the elevator._

" _No!" she screeched. "I need it! I can't lose it!"_

" _I'm not letting you die," Fitz shouted, pulling her into the elevator._

 _The doors sealed shut behind them and the metal box began to descend. Jemma started to panic in her head. Today was the day she was going to unlock his memories, and of course aliens had decided to invade while he was still human. Now she had lost the watch, and with that the life of Time-Lord._

* * *

 _After the invasion ended, another scientist beat Jemma up to her floor. He saw the watch, and decided to snatch it up to sell to pay off some gambling debts. Once he had sold the watch to a pawnshop and gotten the money, he forgot about the watch. But the pawnshop owner soon closed shop in New York and moved across the country to open up a new one in Los Angles. Soon after, a young woman entered his shop one day to see the things in his shop, out of hopes that some might be of alien origin. Unfortunately, she found nothing, but did purchase the pocket watch on the chain._

 _Months later, the same girl found herself in SHIELD custody, on a plane that held a man who was really an alien whose memories were inside that watch._

* * *

 _2014_

"Will they get in here?" Skye asked frantically as Simmons pushed her and Fitz into the lab, sealing the doors shut after they were all in. "Can it keep them out?"

Simmons pursed her lips nervously and fell silent. Skye could hear the alien invaders running about on the floor above them. Thankfully, everyone else on the team was still at the Hub. But in their haste to get away from the invaders, they had decided to lock down the Bus, preventing anyone from getting inside to help them.

"Simmons," she repeated a little louder. "Can it keep them out?"

The biochemist looked up at her. Skye froze when she saw the other girl was crying.

"I had one job," Simmons sniffled, wiping her eyes. "I just had to keep him safe, so he could remember when it was time. But I failed."

"What are you talking about?" Skye asked, crossing her arms. "Who's he?"

Simmons sighed and inhaled deeply. "Might as well tell you, since we're probably going to die and he should know who he really is."

She was looking at Fitz as she said this. Puzzled, Skye frowned. Fitz looked like he was just as confused as her. "I don't have any idea what she's talking about," he mumbled, gazing up at the ceiling anxiously.

"It's because you don't remember, that's all," Simmons said, walking over to him. "You had to become human to escape Sarnim, and to do that, you had to forget who you were."

Fitz took a step back from her. "I know exactly who I am, Simmons! And it's not funny to make jokes when we're about to die down here!"

"But it's not a joke," the biochemist protested. Skye sat down on one of the stools, watching the conversation play out while growing increasingly confused with what was happening. "Fitz, I'm telling the truth, honest! Leo Fitz has only existed for a couple years. But you're really someone else. You're the Doctor."

"The Doctor?" Fitz raised an eyebrow. "Doctor Who?"

"It's just the Doctor," Simmons replied with a chuckle. "You're not from Earth. You're an alien who can travel through time and space in a box called the TARDIS. A few years ago, you saved my life, and invited me to come and travel with you. Do you remember any of this?"

Fitz shook his head slowly, studying his best friend warily.

Skye stood up and stepped forward. "Is there any way you have to prove this to us?" Skye asked, fingering her necklace.

Simmons sighed, her face falling. "When you took away your memories, you put them into a pocket watch and told me to keep it safe. And I did, I really did. But when we went to New York to go work at the SHIELD facility there for a month, which was when the Chitauri attacked. I lost it when we were evacuating to the bunkers. I'm sorry, but it's gone. I looked everywhere, but I couldn't find it."

"You said this happened in New York during the battle, right?" Skye asked, looking down at the watch at the end of the chain around her neck.

Simmons nodded. Skye took a deep breath. "What did it look like?"

"Round, kind of a dull gold color," her friend replied. "There were a lot of circles etched on it. Some of them overlapped, others were inside each other-"

"Like this?" Skye pulled off the necklace and held it up so they could see the watch at the end of it. "I got it in a pawnshop in LA. The owner had moved out there from New York after the battle. I wanted to know if he had anything from the battle that was alien, but he didn't. Had a lot of stuff that was found in the aftermath though. This was one of those items."

Simmons took the watch and inspected it. A smile slowly crept across her face before she hugged Skye tightly. "This is it! Oh, thank you, Skye! You actually found it!"

"Great, so now what happens?" Skye gasped through the embrace, eyeing Fitz. "Does he need to do something?"

"He has to open it," Simmons told her, pulling back and moving toward Fitz. However, the engineer took a step back from her as she approached him.

"Doctor, please," Simmons said softly. "Take it. It's yours."

"It does look familiar…" Fitz murmured. "But no. I'm not doing this. I'm not your…I'm not this Doctor."

"Yes, you are!" Simmons protested, putting the watch in his hand. "You just don't remember that you are. But if you open it, then you will."

"Hey, guys?" Skye pointed to the doors. The invaders of the Bus had arrived in the cargo bay, lining up so they faced the lab doors. All had weapons, or at least they looked like weapons, drawn out. She looked back at Simmons and Fitz with worry. "Any of you know what those are?"

"Bad, very bad," Fitz said quickly, but confidently. "Those are Milurians. Distant relative of Silurians. The weapons they have are Sontarian designed. Milurians are one of the few races who trade with them. Very rare Milurians go on the offensive, though. You've had to do something very, very bad to them to make them this angry and come after you…"

He exhaled sharply and gazed down at his hand. Skye could see the watch visibly clutched tightly in it.

"What was that?" Fitz sounded frightened. "I just…it all suddenly came to me. Was that him?"

Simmons nodded. Fitz gulped, looking down at the watch with fear. He sank to the floor, his back against the Holotable. Skye sat down beside him.

"I'm scared," he admitted. "I'm afraid to open it now. What if I do and I forget you? What I forget that I was ever Leo Fitz? I mean, I want to believe that it's all a big joke, but…Simmons's can't lie. I'm this person I can't even remember, and I don't want to open this if I forget who I am now."

Skye turned her eyes to the floor, understanding his fears. As she turned to say something reassuring to him, a violent force suddenly threw her on top of Fitz while a large boom echoed in the background. The lab doors were now marred by a large, splintering crack, probably from the Milurian weapons. If they took another hit, then their defenses would be done for.

"If you're going to open the watch, please do it now!" Simmons yelped, crawling out from underneath one of the tables. "The doors won't be able to take another hit!"

Fitz looked down at the watch in his palm. Skye grasped his other hand. "You can do this. You'll be okay."

"Thank you," he said, getting to his feet. His finger pressed the catch to open it. Immediately, the face of the watch was exposed. Golden light began to rise out of it in the form of some kind of wispy mist.

"How did he do that?" Skye hissed over at Simmons as the golden wisps began to surround his head. Both girls were watching the display in fascination.

"The Doctor sealed it so only he could open it," explained Simmons, getting onto her knees and rummaging around in a drawer for something.

The light surrounding Fitz suddenly seemed to seep into his skin. His eyes closed, and he clenched his fists. Skye watched him, spellbound. Then Fitz relaxed, and reopened his eyes. He looked exactly the same as before. Had it not worked?

"Well, that's much better," he said, stretching out and smiling. "Oh good, I go remember. That's very good, brilliant really. There's bad outside, so good is helpful."

Skye let out the breath she hadn't realized she'd been holding in. Looking closer at him, she could see that his eyes, while the same, now had an older look to them. They had seen many things, great and terrible. "Doctor?"

"Aha! Yes, yes I am," Fitz- the Doctor smiled at her. "By the way, thank you for finding the watch. Never even knew what was inside, but then again, I didn't remember anything. But we can discuss that later. Now, what's going on outside."

"You said they were Milurians," Simmons said, stepping forward and handing the Doctor a slender object. "I'm so glad you're back, Doctor, and I'm sorry that I lost the watch."

"Don't worry about that, I'm here now, everything's fine," The Doctor reassured her, waving his hand. "Now, the best thing we can do right now is to figure out what they want. So we're going to ask them."

Holding out the object, he pressed something on it. The doors of the lab slide open, and the girls stepped back.

"Hopefully," the Doctor said, pocketing his sonic. "This will end without a war."

* * *

Lucky for them, there was no war. A few days ago, a pod had crash landed on Earth with a bunch of odd, grayish egg-like rocks nestled protectively inside. They were Milurian eggs, being transported across the galaxy by smugglers with the Milurians in pursuit. After the lizard species grew a little too close for the smugglers' liking, they sent the eggs down to Earth in an escape pod with the intent of retrieving them later. The Milurians did manage to catch up with the smugglers and took control of their spacecraft, intent on finding what had been taken from them.

Their SHIELD team had investigated the crash, and Simmons and the Doctor/Fitz had taken the eggs, which they believed to be rocks, back onto the Bus to study. The Milurians had located the signal and followed them. Once this was all cleared up and both parties understood what had happened, the eggs were returned to the rightful species, who then left the Bus and Earth. Skye, along with some help from the Doctor, took the Bus off lockdown while Jemma went to go get the TARDIS, whatever that was. Skye found out when she went down into the cargo bay.

"What the heck is that?" she squawked as she stared at the police box now occupying a space in front of Lola.

"It's a police telephone box. The TARDIS's disguise," The Doctor explained jovially as he patted the side of the blue box and straightened his dark green jumper. There was something more confident about the person she once knew as Fitz, and it was interesting and unnerving at the same time.

"Yeah, but-but how did you get it down here?" Skye stammered, looking at it. There was no way that it could fit through the door by the staircase, and the cargo ramp hadn't been opened.

"It was in my bunk."

"Your bunk isn't big enough to fit that in."

"It is when the TARDIS is miniaturized," Simmons cut in as she swept up the broken glass. "River showed me some of the TARDIS protocols a while back. This was one of them. I did it after he became human and we arrived on Earth. He never knew how to do it until River showed us. She's amazing."

"Who's River?" Skye asked, curious. She loved the name. It was unique, like hers.

"Depending on when you meet her, she's Professor or Doctor River Song. A time traveler, and his wife too."

"His wife, eh?" Skye grinned to herself. It was weird to picture Fitz (she still thought of him as Fitz) married.

"Right, everything looks good to go, and I guess we'll be heading off now," the Doctor announced, peeking his head out the door. Skye had been so caught up in talking with Simmons that she barely noticed him enter the box. "Ready to go, Jemma?"

"You're leaving?" Skye was disappointed now. She had grown close to the two of them. Watching them leave to go explore time and space was going to be sad for her.

"Actually," Simmons spoke up, dragging her foot in front of her in a small arc. "I think I'm going to stay here."

The Doctor's face fell. "You-you are?"

"Yes, I am." The biochemist sighed and crossed her arms. "I loved the adventure and the thrill of traveling with you, but I feel like it's been enough. I've seen a lot, and I'm afraid of messing up again. I almost lost you, Doctor."

The Doctor opened his mouth to reply.

"Doctor?!"

Coulson and May were hurrying up the cargo ramp toward them. All three of them turned their heads toward the newcomers, and their expressions turned to shock as May suddenly hugged the Doctor.

"I can't believe you're here!" the normally stern agent said happily. "I knew it was you!"

"Erm, Agent May, do you mind perhaps letting me go?" the Doctor gasped. "I don't know if I can regenerate again. The last two times were lucky enough for me too."

May backed away, and the Doctor sucked in a lungful of air. "Better. Now how do you know me?"

May looked at Coulson, who laid a hand on her shoulder. She put her own hand on top of his.

"Don't you remember us? Me and Phil?" May sounded confused, and a little upset. This was getting really weird now. Well, weirder.

Coulson cleared his throat. "How old are you?"

"Two thousand eight hundred and nine, approximately." Skye started to snigger as the Doctor shot her a dirty look. "Yes, I know. I'm old."

"Oh." May looked like she'd finally realized something. "You don't know us yet. Timey-wimey."

"Shush, spoilers!" The Doctor put a finger to his lips as Ward entered the cargo hold. "Oh brilliant! Now River's rubbing off on me."

"What's that?" The specialist frowned and pointed at the TARDIS. "What's going on?"

"We'll tell you later," Coulson said, sharing a smile with May.

The Doctor's face was now much sadder as he gazed around the room. Skye stepped forward, and he noticed the movement. He smiled at her. "Skye? You fancy a trip with me?"

"Where? And how?"

"Anywhere in time and space that you want, and we'll be just brilliant in this."

The Doctor patted the side of the TARDIS, grinning like a little kid.

"In that tiny box?" Skye couldn't believe it. "We'll barely fit!"

"Oh, you'll fit just fine," Coulson said with a laugh. "You see, it's-"

"Shush, don't spoil it!" It was funny to see the Doctor snapping his fingers at Coulson to keep him quiet. "Let her figure it out for herself."

He turned back to her. "So what do you say?"

"It sounds like fun, but I'm in the middle of training-"

"Skye, you're pretty much qualified for the field," Coulson told her, smiling. May had a mischievous expression on her features. "This is the adventure of a lifetime, and you don't want to let this go. Trust us, we know."

Skye grinned and leapt forward to hug them. "I hope you're right," she told them. "Thank you!"

"Don't thank us," May chuckled. "Hopefully you'll be seeing _us_ quite soon."

Skye hugged Simmons and Ward goodbye before skipping back to where the Doctor stood beside the TARDIS. "See you guys later."

"Goodbye, Jemma," The Doctor said as his former companion came forward and hugged him. He gave a salute to Ward. "Ward, you take care of her, or I'll come back and drop you into a mess of Daleks."

"Doctor!"

"What's a Dalek?"

"You don't want to find out," May replied, giving the Time-Lord a stony look.

"Fine," The Doctor sighed, sounding a bit disappointed. "No Daleks, but you be good to her."

He pointed two fingers to his eyes and then out at Ward.

Ward nodded, looking a bit more nervous. "Yes…Doctor?"

The Doctor nodded in approval before turning his attention to May and Coulson. "I hope to see you two again someday."

"We hope so too," Coulson said, reaching out to shake hands with the Doctor. May gave him another hug before he pulled a key out of his pocket and unlocked the doors to the TARDIS.

"Skye, if you'll just come in here," he said, pushing the door in and stepping inside.

With one last wave, Skye stepping inside the box, expecting to b cramped in a tiny space with the Doctor. Instead, she was in an incredibly spacious room. The walls were silvery with odd round things punched into them. A staircase led down to the center of the room, where there was a console of sorts covered with a variety of levers, buttons, switches, and even a bell. Skye gaped at everything, taking it all in.

"Any passing remarks?" The Doctor asked, tying a tie that seemed to have monkeys on it around his neck. "Anything you want to say?"

"It's… it's bigger on the inside?"

"There we go! Brilliant!" The Doctor climbed up the staircase and led her down to the console. "So, quick bit of information. TARDIS. Time And Relative Dimension In Space. This old girl allows us to travel through time and space. Anywhere, anytime. It's your choice on where we go. So where will it be?"

Skye thought it over for a moment. "Know of anything really extraordinary?"

"Oh sure. Are you fine with going outside this galaxy?"

Skye nodded. The Doctor began to press a variety of switches and pulled a few levers. "You might want to hang on to something."

* * *

Outside the TARDIS, May, Coulson, Simmons, and Ward listened to the wheezing groan as the TARDIS disappeared in the cargo bay. The first three knew about this effect, but Ward was stunned. "Can someone tell me what's going on?"

Simmons chuckled and shook her head. "C'mon, I'll tell you upstairs."

She lead him up the staircase, leaving May and Coulson by themselves in the cargo bay.

The latter turned to the former. "How long do you think they'll be traveling until they met up with us?"

* * *

 **So what do you all think? Anyone want another one of these, maybe featuring another SHIELD person as the Master?**


	2. Chapter 2

Hello all! I'd like to announce that I finally wrote another little bit in this series. It's call 'One Last Trip Home', and it features Clara Oswald, Skye, and the Thirteenth Doctor/Fitz. IF you're interested, have a read. It's in the crossover section for Agents of SHIELD and Doctor Who.


	3. Chapter 3

Happy Holidays! I've written a Christmas-y story for this universe. It's called 'We Hit Lola'

Yes, you read that right.


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